Zhiyi Li

Dominic Masters, Josef Dean, Kerstin Klaser et al.

We present GPS++, a hybrid Message Passing Neural Network / Graph Transformer model for molecular property prediction. Our model integrates a well-tuned local message passing component and biased global attention with other key ideas from prior literature to achieve state-of-the-art results on large-scale molecular dataset PCQM4Mv2. Through a thorough ablation study we highlight the impact of individual components and find that nearly all of the model's performance can be maintained without any use of global self-attention, showing that message passing is still a competitive approach for 3D molecular property prediction despite the recent dominance of graph transformers. We also find that our approach is significantly more accurate than prior art when 3D positional information is not available.

Zhiyi Li, Shengjie Zhang, Yujie Song et al.

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can facilitate the extraction and analysis of important biomedical information, which can be used to improve downstream applications including the healthcare system. However, NER in the biomedical domain is challenging due to limited data availability, as the high expertise, time, and expenses are required to annotate its data. In this paper, by using the limited data, we explore various extrinsic factors including the corpus annotation scheme, data augmentation techniques, semi-supervised learning and Brill transformation, to improve the performance of a NER model on a clinical text dataset (i2b2 2012, \citet{sun-rumshisky-uzuner:2013}). Our experiments demonstrate that these approaches can significantly improve the model's F1 score from original 73.74 to 77.55. Our findings suggest that considering different extrinsic factors and combining these techniques is a promising approach for improving NER performance in the biomedical domain where the size of data is limited.